The Simulator That Isn't There

Okay, this is one of those cases where I kvetch about other people not having built the tools I want to use - perhaps a bit of a insufferably egotistical position.  I mean, what gives me the chutzpah to do that?  My title, according to me, is "Automation Visioneer", so that gives me the right - though again, self-given title, self-given right.  But I hope you'll bear with me, because I think (there again, me! me! me!) it is an interesting observation on a curious gap in the software world - one that could make a very interesting project for someone so inclined. Oh, and this is one of the "a bit of promoting the product" entries - which means I get to blog on company time.

Countable Labs Raises Funds, Heads to Clinic

I caught up by teleconference recently with Countable Labs CEO Giovanna Prout, fresh off Countable Labs' $26M equity fundraising - a round which was oversubscribed.  Top on my agenda: what is Prout's vision to turn that money into products.  And how will Countable balance building molecular tools vs. applying those tools to clinical problems?

Alex Hastie Returns to BioNano, Takes CSO Reins

An interesting news item this week is that BioNano Genomics has appointed Alex Hastie as Chief Scientific Officer.  Hastie is an obvious choice for CSO, as for many years he was very much the public scientific face of BioNano's development.  .  But in February 2025 he left BioNano and headed to Arima Genomics.  But after a bit over a year at Arima and then a short stint at Inocras, Hastie has returned to the fold.

E.coli Doesn't Like Diets Either, At Least Genomic Ones

Another interesting preprint that fits several recent themes - genome minimization, discontinuation of products - comes from a Japanese group that reports on significantly reducing the genome of E.coli.  They tried for 1.7Mb but ended up settling - for now - with a 2.3Mb genome.  That's only about half the size of the strain they started with, but not at all a small genome.  

Shredding Genomes: Establishing Plausible Deletability

There's an interesting new preprint from Jay Shendure's lab which introduces the technique of Shred-Seq, which is a Cas3-driven approach to generating large deletions across a large eukaryotic genome.  By creating diverse collections of deletions, Shred-Seq enables identifying hidden non-coding sequences of functional importance.

The Commercial End for Fluidigm Technology?

Last week brought news that Standard Biotools, which is what Fluidigm morphed into, is being acquired by Treeline Biosciences, a drug developer.  The deal values Standard at about its cash position - and Treeline made it immediately clear this is a reverse merger to grab the cash and in effect go public by also grabbing Standard's stock listing.  What Treeline has made very clear is that they have absolutely no interest in is Standard's existing tools portfolio.

Long Reads for Rare Diseases Hits New England Journal of Medicine

Alexander Hoischen and colleagues have a brief piece in New England Journal of Medicine that published early this morning, in conjunction with the European Society of Human Genomics (ESHG) meeting.  I'm now in the thrall of ESHG FOMO - I attended last year in part because it was immediately after London Calling and it seemed silly not to extend my trip (plus Alex had asked me personally to go), but this year I reluctantly decided my travel load was getting high and decided to make only one transatlantic flight in the May-June timeframe.  Hopefully I picked the right one.  The piece is the latest installment of a long running program to demonstrate that long read sequencing, specifically PacBio HiFi sequencing, can replace a battery of older tests when trying to diagnose rare genetic diseases.